# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:11:25 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-bromo-4-methylphenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Br)c([O-])c(c1)c2[nH]c3ccc(cc3n2)C(N)=[NH2+]
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 334  334  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-bromo-4-methylphenolate  ligand  34  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_334
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 334  C1    C   CR6    0  -0.003  -4.9140  -0.2223  -0.0712
 334  C2    C   CR16   0  -0.296  -4.5540  -1.5675   0.1311
 334  C3    C   CR16   0  -0.304  -3.2309  -1.9392   0.2738
 334  C4    C   CR56   0   0.359  -2.2799  -0.9282   0.2223
 334  C5    C   CR56   0   0.171  -2.6227   0.4291   0.0273
 334  C6    C   CR16   0  -0.375  -3.9544   0.7869  -0.1289
 334  C7    C   C      0   0.580  -6.3294   0.1257  -0.2241
 334  N1    N   NH2    0  -0.769  -7.2366  -0.5305   0.4620
 334  N2    N   NC2    1  -0.767  -6.6733   1.0910  -1.0449
 334  N3    N   NR15   0  -0.728  -0.9289  -0.9237   0.3358
 334  N4    N   N      0  -0.503  -1.4997   1.2063   0.0326
 334  C8    C   CR5    0   0.495  -0.5008   0.3662   0.2177
 334  C1'   C   CR6    0  -0.222   0.9039   0.7089   0.2975
 334  C2'   C   CR16   0  -0.338   1.2748   2.0547   0.1964
 334  C3'   C   CR6    0   0.061   2.5890   2.4712   0.2614
 334  CV'   C   CH3    0  -0.722   2.9779   3.9168   0.1296
 334  C4'   C   CR16   0  -0.258   3.5678   1.4816   0.4387
 334  C5'   C   CR6    0  -0.267   3.2224   0.1558   0.5415
 334  C6'   C   CR6    0   0.369   1.8770  -0.3332   0.4803
 334  O6'   O   OC    -1  -0.577   1.5953  -1.5602   0.5812
 334  BR5'  BR  BR     0  -0.106   4.5766  -1.1470   0.7866
 334  HC2   H   HCR6   0   0.272  -5.3155  -2.3359   0.1432
 334  HC3   H   HCR6   0   0.275  -2.9567  -2.9761   0.4127
 334  HC6   H   HCR6   0   0.273  -4.2281   1.8269  -0.2566
 334  HH11  H   HNH2   0   0.443  -6.9665  -1.1668   1.1939
 334  HH12  H   HNH2   0   0.435  -8.2246  -0.3663   0.3408
 334  HH21  H   HNC2   0   0.435  -7.6249   1.4156  -1.1246
 334  HH22  H   HNC2   0   0.444  -5.9989   1.4963  -1.6731
 334  HN3   H   HNR5   0   0.421  -0.2527  -1.6740   0.4759
 334  HC2'  H   HCR6   0   0.238   0.4898   2.7912   0.0661
 334  H32'  H   HCH3   0   0.235   3.4193   4.1326  -0.8461
 334  H33'  H   HCH3   0   0.238   2.1124   4.5691   0.2433
 334  H34'  H   HCH3   0   0.235   3.7115   4.2096   0.8825
 334  HC4'  H   HCR6   0   0.258   4.6103   1.7751   0.4969

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 334  C1   C2    aromatic  1.407  0.020  1.407
 334  C1   C6    aromatic  1.394  0.020  1.394
 334  C1   C7    single    1.466  0.020  1.466
 334  C2   C3    aromatic  1.382  0.020  1.382
 334  C2   HC2   single    0.930  0.020  1.080
 334  C3   C4    aromatic  1.389  0.020  1.389
 334  C3   HC3   single    0.930  0.020  1.080
 334  C4   C5    aromatic  1.413  0.020  1.413
 334  C4   N3    aromatic  1.356  0.020  1.356
 334  C5   C6    aromatic  1.388  0.020  1.388
 334  C5   N4    aromatic  1.366  0.020  1.366
 334  C6   HC6   single    0.930  0.020  1.080
 334  C7   N1    single    1.313  0.020  1.313
 334  C7   N2    double    1.313  0.020  1.313
 334  N1   HH11  single    0.860  0.020  1.020
 334  N1   HH12  single    0.860  0.020  1.020
 334  N2   HH21  single    0.860  0.020  1.020
 334  N2   HH22  single    0.860  0.020  1.020
 334  N3   C8    aromatic  1.364  0.020  1.364
 334  N3   HN3   single    0.860  0.020  1.020
 334  N4   C8    aromatic  1.318  0.020  1.318
 334  C8   C1'   single    1.448  0.020  1.448
 334  C1'  C2'   aromatic  1.400  0.020  1.400
 334  C1'  C6'   aromatic  1.437  0.020  1.437
 334  C2'  C3'   aromatic  1.380  0.020  1.380
 334  C2'  HC2'  single    0.930  0.020  1.080
 334  C3'  CV'   single    1.503  0.020  1.503
 334  C3'  C4'   aromatic  1.403  0.020  1.403
 334  CV'  H32'  single    0.970  0.020  1.090
 334  CV'  H33'  single    0.970  0.020  1.090
 334  CV'  H34'  single    0.970  0.020  1.090
 334  C4'  C5'   aromatic  1.374  0.020  1.374
 334  C4'  HC4'  single    0.930  0.020  1.080
 334  C5'  C6'   aromatic  1.433  0.020  1.433
 334  C5'  BR5'  single    1.895  0.020  1.895
 334  C6'  O6'   single    1.263  0.020  1.263

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 334  C7    C1   C6    119.25  3.000
 334  C7    C1   C2    119.28  3.000
 334  C6    C1   C2    121.47  3.000
 334  HC2   C2   C3    118.81  3.000
 334  HC2   C2   C1    120.03  3.000
 334  C3    C2   C1    121.13  3.000
 334  HC3   C3   C4    121.94  3.000
 334  HC3   C3   C2    120.93  3.000
 334  C4    C3   C2    117.13  3.000
 334  N3    C4   C5    104.48  3.000
 334  N3    C4   C3    132.97  3.000
 334  C5    C4   C3    122.55  3.000
 334  N4    C5   C6    130.00  3.000
 334  N4    C5   C4    110.27  3.000
 334  C6    C5   C4    119.73  3.000
 334  HC6   C6   C5    120.22  3.000
 334  HC6   C6   C1    121.75  3.000
 334  C5    C6   C1    117.99  3.000
 334  N2    C7   N1    120.87  3.000
 334  N2    C7   C1    119.52  3.000
 334  N1    C7   C1    119.61  3.000
 334  HH12  N1   HH11  116.94  3.000
 334  HH12  N1   C7    122.17  3.000
 334  HH11  N1   C7    120.69  3.000
 334  HH22  N2   HH21  116.94  3.000
 334  HH22  N2   C7    120.70  3.000
 334  HH21  N2   C7    122.22  3.000
 334  HN3   N3   C8    119.97  3.000
 334  HN3   N3   C4    132.06  3.000
 334  C8    N3   C4    107.97  3.000
 334  C8    N4   C5    105.13  3.000
 334  C1'   C8   N4    126.30  3.000
 334  C1'   C8   N3    121.56  3.000
 334  N4    C8   N3    112.14  3.000
 334  C6'   C1'  C2'   121.80  3.000
 334  C6'   C1'  C8    119.48  3.000
 334  C2'   C1'  C8    118.73  3.000
 334  HC2'  C2'  C3'   119.34  3.000
 334  HC2'  C2'  C1'   118.03  3.000
 334  C3'   C2'  C1'   122.62  3.000
 334  C4'   C3'  CV'   120.59  3.000
 334  C4'   C3'  C2'   117.22  3.000
 334  CV'   C3'  C2'   122.18  3.000
 334  H34'  CV'  H33'  107.53  3.000
 334  H34'  CV'  H32'  106.95  3.000
 334  H33'  CV'  H32'  107.21  3.000
 334  H34'  CV'  C3'   111.82  3.000
 334  H33'  CV'  C3'   111.17  3.000
 334  H32'  CV'  C3'   111.90  3.000
 334  HC4'  C4'  C5'   119.91  3.000
 334  HC4'  C4'  C3'   119.11  3.000
 334  C5'   C4'  C3'   120.97  3.000
 334  BR5'  C5'  C6'   116.22  3.000
 334  BR5'  C5'  C4'   119.57  3.000
 334  C6'   C5'  C4'   124.21  3.000
 334  O6'   C6'  C5'   122.52  3.000
 334  O6'   C6'  C1'   124.30  3.000
 334  C5'   C6'  C1'   113.18  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 334  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 334  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 334  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 334  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 334  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 334  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 334  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 334  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 334  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 334  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 334  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 334  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 334  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 334  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 334  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 334  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 334  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 334  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 334  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 334  CONST_20  C2'   C1'  C8   N3    180.00   0.0  0
 334  CONST_21  C6'   C1'  C8   N3      0.00   0.0  0
 334  CONST_22  C2'   C1'  C8   N4      0.00   0.0  0
 334  CONST_23  C6'   C1'  C8   N4    180.00   0.0  0
 334  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 334  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 334  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 334  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 334  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 334  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 334  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 334  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 334  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 334  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 334  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 334  CONST_35  CV'   C3'  C2'  C1'   180.00   0.0  0
 334  CONST_36  BR5'  C5'  C6'  C1'   180.00   0.0  0
 334  CONST_37  O6'   C6'  C1'  C2'   180.00   0.0  0
 334  CONST_38  BR5'  C5'  C4'  C3'   180.00   0.0  0
 334  CONST_39  C5'   C4'  C3'  CV'   180.00   0.0  0
 334  CONST_40  O6'   C6'  C5'  C4'   180.00   0.0  0
 334  CONST_41  HC3   C3   C2   C1    180.00   0.0  0
 334  CONST_42  HC6   C6   C1   C2    180.00   0.0  0
 334  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 334  CONST_44  HC2   C2   C3   C4    180.00   0.0  0
 334  CONST_45  HC2'  C2'  C1'  C8      0.00   0.0  0
 334  CONST_46  HC4'  C4'  C3'  C2'   180.00   0.0  0
 334  CONST_47  HH11  N1   C7   C1      0.00   0.0  0
 334  CONST_48  HH12  N1   C7   C1    180.00   0.0  0
 334  CONST_49  HH21  N2   C7   C1    180.00   0.0  0
 334  CONST_50  HH22  N2   C7   C1      0.00   0.0  0
 334  Var_01    N1    C7   C1   C2     35.45  30.0  2
 334  Var_02    H32'  CV'  C3'  C2'  -105.04  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 334  plan-1  C8    0.020
 334  plan-1  C1'   0.020
 334  plan-1  C2'   0.020
 334  plan-1  C3'   0.020
 334  plan-1  CV'   0.020
 334  plan-1  C4'   0.020
 334  plan-1  C5'   0.020
 334  plan-1  C6'   0.020
 334  plan-1  O6'   0.020
 334  plan-1  BR5'  0.020
 334  plan-1  HC2'  0.020
 334  plan-1  HC4'  0.020
 334  plan-2  C1    0.020
 334  plan-2  C2    0.020
 334  plan-2  C3    0.020
 334  plan-2  C4    0.020
 334  plan-2  C5    0.020
 334  plan-2  C6    0.020
 334  plan-2  C7    0.020
 334  plan-2  N3    0.020
 334  plan-2  N4    0.020
 334  plan-2  C8    0.020
 334  plan-2  C1'   0.020
 334  plan-2  HC2   0.020
 334  plan-2  HC3   0.020
 334  plan-2  HC6   0.020
 334  plan-2  HN3   0.020
 334  plan-3  C1    0.020
 334  plan-3  C7    0.020
 334  plan-3  N1    0.020
 334  plan-3  N2    0.020
 334  plan-3  HH11  0.020
 334  plan-3  HH12  0.020
 334  plan-3  HH21  0.020
 334  plan-3  HH22  0.020

